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Environment modules

In order to provide multiple versions of software compiled with different and varying libraries, we use modules. Modules allow us to add and remove software from our $PATH using a simple module command.

Common usage

  • module avail [name] View all the modules on the HPC system filtered by name.
  • module list View currently loaded modules
  • module load moduleName Load the module denoted by moduleName
  • module purge Unload all loaded modulefiles

Loading the R module

First we want to take a look at what R modules are available. To do that issue:

module avail R

[john@discovery7 ~]$ module avail R

--------------------- /dartfs-hpc/admin/opt/modules/el7 ----------------------
R/4.0            R/4.0.4(default) R/4.1.2

As you can see from this output there are multiple versions of R available. The one with (default) next to it is the default module and will be picked unless you specify the full path. For example, if I wanted R/4.1.2 I would issue:

module load R/4.1.2

If I did not care about what version I recieved then I can just issue module load R.

module load R

Once you have loaded the module you would like you can issue module list to see what you have currently loaded.

module list

[john@discovery7 ~]$ module load R
[john@discovery7 ~]$ module list
Currently Loaded Modulefiles:
  1) R/4.0.4

Since I did not specify a version, the module command pulled in the (default) version of R, which happens to be R/4.0.4